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(-) Description

Title :  CRYSTAL STRUCTURE OF URIDYLATE KINASE FROM ARCHAEOGLOBUS FULGIDUS
 
Authors :  Y. Patskovsky, R. Chen, L. J. Keefe, J. M. Sauder, M. Dickey, J. M. Adams, S. R. Wasserman, S. K. Burley, S. C. Almo, New York Sgx Research Cen Structural Genomics (Nysgxrc)
Date :  29 Sep 06  (Deposition) - 17 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Kinase, Structural Genomics, Protein Structure Initiative, Psi, Nysgxrc, New York Sgx Research Center For Structural Genomics Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, R. Chen, L. J. Keefe, J. M. Sauder, M. Dickey, J. M. Adams S. Ozyurt, S. R. Wasserman, S. K. Burley, S. C. Almo
Crystal Structure Of Uridylate Kinase From Archaeoglobus Fulgidus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - URIDYLATE KINASE
    Chains: A, B
    EC Number: 2.7.4.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PYRH, AF_2042
    Mutation: YES
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 224325
    Strain: DSM 4304
    Synonym: UK, URIDINE MONOPHOSPHATE KINASE, UMP KINASE, PUTATIVE DEHYDRATASE PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:8 , GLY A:9 , GLY A:40 , GLY A:41 , ARG A:46 , THR A:116BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREGLY B:8 , GLY B:9 , GLY B:40 , GLY B:41 , GLY B:42 , ARG B:46 , THR B:116BINDING SITE FOR RESIDUE SO4 B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2IJ9)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ser A:168 -Arg A:169
2Gly A:175 -Thr A:176
3Asp B:145 -Pro B:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2IJ9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2IJ9)

(-) Exons   (0, 0)

(no "Exon" information available for 2IJ9)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:214
 aligned with PYRH_ARCFU | O28237 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
           PYRH_ARCFU     1 MKVVLSLGGSVLSNESEKIREFAKTIESVAQQNQVFVVVGGGKLAREYIKRARELGASETFCDYIGIAATRLNAMLLISAIPSAAKKVPVDFMEAEELSKLYRVVVMGGTFPGHTTDATAALLAEFIKADVFINATNVDGVYSADPKSDTSAVKYDRLSPQQLVEIVSRSSAKAGTNVVIDLLAAKIIERSKIKTYVILGTPENIMKAVKGEAVGTVIA 219
               SCOP domains d2ij9a1 A:1-219 Uridylate kinase PyrH                                                                                                                                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......hhhhhhhhhhhhhhhhhhheeeeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh...eeee........hhhhhhhhhhhh...eeeeee....................eehhhhhhhhh..-----......hhhhhhhhhhhh..eeeee.hhhhhhhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ij9 A   1 MKVVLSLGGSVLSNESEKIREFAKTIESVAQQNQVFVVVGGGKLAREYIKSARELGASETFCDYIGIAATRLNAMLLISAIPSAAKKVPVDFMEAEELSKLYRVVVMGGTFPGHTTDATAALLAEFIKADVFINATNVDGVYSADPKSDTSAVKYDRLSPQQLVEIVSR-----GTNVVIDLLAAKIIERSKIKTYVILGTPENIMKAVKGEAVGTVIA 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        |-    |  180       190       200       210         
                                                                                                                                                                                                  169   175                                            


Chain B from PDB  Type:PROTEIN  Length:216
 aligned with PYRH_ARCFU | O28237 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
           PYRH_ARCFU     1 MKVVLSLGGSVLSNESEKIREFAKTIESVAQQNQVFVVVGGGKLAREYIKRARELGASETFCDYIGIAATRLNAMLLISAIPSAAKKVPVDFMEAEELSKLYRVVVMGGTFPGHTTDATAALLAEFIKADVFINATNVDGVYSADPKSDTSAVKYDRLSPQQLVEIVSRSSAKAGTNVVIDLLAAKIIERSKIKTYVILGTPENIMKAVKGEAVGTVIA 219
               SCOP domains d2ij9b_ B: Uridylate kinase PyrH                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......hhhhhhhhhhhhhhhhhhheeeeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh...eeee........hhhhhhhhhhhh...eeeeee....................eehhhhhhhhh....---......hhhhhhhhhhhh..eeeee.hhhhhhhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ij9 B   1 MKVVLSLGGSVLSNESEKIREFAKTIESVAQQNQVFVVVGGGKLAREYIKSARELGASETFCDYIGIAATRLNAMLLISAIPSAAKKVPVDFMEAEELSKLYRVVVMGGTFPGHTTDATAALLAEFIKADVFINATNVDGVYSADPKSDTSAVKYDRLSPQQLVEIVSRSS---GTNVVIDLLAAKIIERSKIKTYVILGTPENIMKAVKGEAVGTVIA 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170|   |  180       190       200       210         
                                                                                                                                                                                                    171 175
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2IJ9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IJ9)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PYRH_ARCFU | O28237)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0033862    UMP kinase activity    Catalysis of the reaction: ATP + UMP = ADP + UDP.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0009041    uridylate kinase activity    Catalysis of the reaction: ATP + (d)UMP = ADP + (d)UDP.
biological process
    GO:0044210    'de novo' CTP biosynthetic process    The chemical reactions and pathways resulting in the formation of cytidine 5'-triphosphate (CTP) from simpler components.
    GO:0046939    nucleotide phosphorylation    The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006221    pyrimidine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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